Hi Benoist-
It is relatively straight-forward to generate both dose-weighted and non-dose-weighted averaged frames outside of the RELION workflow using Unblur / Summovie. You can then create symbolic links to the appropriate set of micrographs (e.g. non-dose-weighted for CTF estimation, and dose-weighted for particle extraction) in RELION’s “Micrographs” directory before initiating that stage of processing. As long as you maintain the same file names, RELION’s star files are agnostic to the contents of the actual images. Please feel free to contact me off-list if you would like more details of how to do this. However, if you are just running the tutorial, it might be faster to simply re-process the data using MotionCorr2.
Best,
-Greg Alushin
On 6/26/17, 12:23 PM, "Collaborative Computational Project in Electron cryo-Microscopy on behalf of Sjors Scheres" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Hi Benoist,
The unblur wrapper does not write out the average without
dose-weighting. So I'm afraid the use of non-dose-weighted averages for
CTF estimation is currently limited to motioncor2. This is merely an
implementation limitation of the wrapper. Not an inherent limitation of
unblur.
HTH,
Sjors
On 06/26/2017 12:47 PM, Benoist LAURENT wrote:
> I used Unblur instead of MotionCor2.
> I did use the relion wrapper.
>
> Is the compatibility with unblur break?
>
> Benoist
>
>
>
>> On 26 Jun 2017, at 13:19, Sjors Scheres <[log in to unmask]> wrote:
>>
>> Hi Benoist,
>> Did you run MotionCor2 through the relion-2.1 wrapper? In that case, the MotionCorr/job002/corrected_micrographs.starshould have 2 columns, one like you have and another one called _rlnMicrographNameNoDW with the _noDW.mrc micrograph (without dose-weighting). You are using the latter to estimate CTFs, but it is not part of your star file. Perhaps this one was made in 2.0? If so, just use the dose-weighted micrograph to estimate CTFs and it should work.
>> HTH,
>> Sjors
>>
>> On 06/26/2017 10:05 AM, Benoist LAURENT wrote:
>>> Hi Sjors,
>>>
>>> Thank you for your answer.
>>>
>>> This is the content of MotionCorr/job002/corrected_micrographs.star:
>>>
>>> $ cat MotionCorr/job002/corrected_micrographs.star
>>>
>>> data_
>>>
>>> loop_
>>> _rlnMicrographName #1
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-14_33_35_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-14_57_34_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-15_14_01_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-15_41_22_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-15_53_09_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-15_56_10_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-16_26_22_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-16_44_07_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-16_55_40_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-16_59_12_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-17_02_43_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-17_14_17_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-17_17_05_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-17_23_32_0.mrc
>>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-17_26_54_0.mrc
>>>
>>> I also checked that the micrographs listed here actually exist, which is the case.
>>>
>>> Any idea?
>>> Best,
>>> Benoist
>>>
>>>
>>>> On 23 Jun 2017, at 13:26, Sjors Scheres <[log in to unmask]> wrote:
>>>>
>>>> Hi Benoist,
>>>> Somehow the micrograph name is empty. How does
>>>>
>>>> MotionCorr/job002/corrected_micrographs.star
>>>>
>>>> look like?
>>>> Sjors
>>>> On 06/23/2017 11:21 AM, Benoist LAURENT wrote:
>>>>> Hi,
>>>>>
>>>>> I want the tutorial to complete Relion21 tutorial to assess if I installed it correctly.
>>>>>
>>>>> At step 3 “CTF estimation”, I get this warning message "WARNING: skipping, since cannot get CTF values for”.
>>>>> Note that the message is not truncated : it stops after “for”.
>>>>>
>>>>> As one could expect this output and from the runtime, which is 0 second, output files are empty.
>>>>>
>>>>> This is the command ran by relion:
>>>>>
>>>>> relion_run_ctffind_mpi --i MotionCorr/job002/corrected_micrographs.star --o CtfFind/job005/ --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 3.54 --Box 512 --ResMin 30 --ResMax 7.1 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --use_noDW --ctffind_exe /usr/local/relion/bin/ctffind --ctfWin -1 —is_ctffind4
>>>>>
>>>>> This is the content of _ctffind4.com:
>>>>>
>>>>> #!/usr/bin/env csh
>>>>> /usr/local/relion/bin/ctffind > CtfFind/jobfoo/_ctffind4.log << EOF
>>>>> CtfFind/jobfoo/
>>>>> CtfFind/jobfoo/.ctf
>>>>> 3.54
>>>>> 300
>>>>> 2
>>>>> 0.1
>>>>> 512
>>>>> 30
>>>>> 7.1
>>>>> 5000
>>>>> 50000
>>>>> 500
>>>>> no
>>>>> no
>>>>> yes
>>>>> 100
>>>>> no
>>>>> no
>>>>> EOF
>>>>> exit 0
>>>>>
>>>>> What I understand from this file is that relion doesn’t give the correct mrc input file to ctffind (c.f. line 3).
>>>>>
>>>>> I’m running ctffind v4.1.8 from Jun 15 2017.
>>>>>
>>>>> Has anyone encountered this problem?
>>>>>
>>>>> I guess there is an obvious misconfiguration problem from my side, but can’t find it.
>>>>>
>>>>> Any help would be greatly appreciated.
>>>>> Best regards.
>>>>> --
>>>>> Benoist Laurent, PhD
>>>>> Research Engineer CNRS
>>>>> Institut de Biologie Physico-Chimique - FRC 550
>>>>> 13, rue Pierre et Marie Curie - F-75005 Paris
>>>>> Tel. +33 [0]1 58 41 52 08
>>>>> --
>>>>> Benoist
>>>>> Room S05 (basement)
>>>>> 52 08
>>>> --
>>>> Sjors Scheres
>>>> MRC Laboratory of Molecular Biology
>>>> Francis Crick Avenue, Cambridge Biomedical Campus
>>>> Cambridge CB2 0QH, U.K.
>>>> tel: +44 (0)1223 267061
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_scheres&d=DwIDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=w6wfhYdHSJtIyhR5sXwmbXTF-kYj6cqUtiN3MLhipb8&m=dN6qmPmfB4Llr9xH1fSGIbDXef_JS4sDnEZHfMkfcsA&s=Lm5YbGvgg6-wJr6YK3osqAwpDf1aLO-oomK0zNsKSWY&e=
>> --
>> Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_scheres&d=DwIDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=w6wfhYdHSJtIyhR5sXwmbXTF-kYj6cqUtiN3MLhipb8&m=dN6qmPmfB4Llr9xH1fSGIbDXef_JS4sDnEZHfMkfcsA&s=Lm5YbGvgg6-wJr6YK3osqAwpDf1aLO-oomK0zNsKSWY&e=
>>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_scheres&d=DwIDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=w6wfhYdHSJtIyhR5sXwmbXTF-kYj6cqUtiN3MLhipb8&m=dN6qmPmfB4Llr9xH1fSGIbDXef_JS4sDnEZHfMkfcsA&s=Lm5YbGvgg6-wJr6YK3osqAwpDf1aLO-oomK0zNsKSWY&e=
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